On Monday, when the magnitude of this week's terrorist attacks translates into the cold, insensitive math of stock prices, some software shares may feel more pain than others. Long a hard-to-stomach aspect of software investing, software firms take in the lion's share of their revenue at the end of the quarter. As the third quarter draws to a close Sept. 30, that means they could be particularly vulnerable as businesses from all sectors try to regroup in the wake of Tuesday's attacks. "This is going to hit software companies especially hard," says Jon Ekoniak, an analyst who covers the software sector for U.S. Bancorp Piper Jaffray. "Most software business comes in September, and all businesses have been hard-hit by the events of this week. We're not even thinking about Q3 anymore. The question now is what's the prospect for Q4." In getting back to business as usual, American companies face hurdles ranging from the mundane to the complex, and they will all take time to work out, observers said. For instance, employees from all walks of life were still scattered across the country Thursday as a ban on air travel was partially lifted. They'll need to get home and assess the situations at their own firms before closing any deals that were in the works. "Fifty to 60 percent of software license sales close in the third month of the quarter, and we all know that nothing got done this week," says Bill Schaff, manager of the $30 million Berger Information Technology fund, which owns software names including Siebel Systems ( SEBL), Oracle ( ORCL) and Microsoft ( MSFT). "They'll be lucky if anything gets done next week. I guarantee you right now in New York, no one is thinking about software application development." Schaff says the slowing of business, already apparent in myriad cancellations of corporate events in September by companies such as Microsoft, SAP ( SAP) and webMethods ( WEBM), could have a dramatic impact on the top and bottom lines of software companies during the third quarter, a fact investors will fret over when trading resumes Monday. "I think there could be some huge misses," Schaff says. "Now mind you, they'll use the attacks as an excuse for Q3 and say that the business will move to Q4, but that doesn't necessarily ring true." Depending on how you look at it, though, the timing of the slowed business could be worse. The third quarter has never been a banner period for the software business because of summer vacations in July and August. On the other hand, the post-Labor Day return-to-work has traditionally given the period somewhat of a boost in its closing month. Now, Schaff says, "It's like summer has been extended, and not for the reasons we like." Of course, slower September software sales are just short-term effects of the tragedy, and market strategists have cautioned investors not to dump shares if a selloff should occur when markets open. Historically, markets have rebounded fairly quickly after initially dipping in the wake of other periods of national loss, including after John F. Kennedy's assassination and Pearl Harbor. Yet it's hard to imagine that investors won't still be calculating the effect of Tuesday's events into share prices long after September in a way that is also particularly relevant to software companies. "This is just the beginning of a horrible period," says Bob Austrian, software analyst at Banc of America Securities. "Software purchases are usually focused on expanding one's scope, and that's not necessarily what businesses will do in the immediate aftermath of this week's tragedy." Instead, businesses likely will want to get back to the basics, bolstering infrastructure and making sure they back up systems already in place. While that could help some software firms like Veritas ( VRTS) and perhaps Oracle, the bells and whistles of business application software might not have the same shimmer they once did. "Applications software is usually about business strategy and/or about cost control, neither of which would be on the chief executive's mind in the coming weeks," Austrian says. "People are going to be busy tending to their most urgent needs." That said, analysts and investors says that large, established software firms have the best chance of surviving the uncertainties ahead. That means companies such as Microsoft, Oracle, SAP, Siebel and perhaps PeopleSoft ( PSFT). Still, in the aftermath of the attacks, gaming the chances of one company over the other is likely a meaningless exercise. As they did to the people of the U.S., Tuesday's attacks will bind the group together as one. "At this point, the sector will be affected as a group," Austrian says. "With the U.S. Capitol being evacuated, airports being shut down and in an environment like this, which of these companies is best and worst is probably hairsplitting." If only we could go back to a time when hairsplitting over stocks seemed an important and worthwhile endeavor.